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comparison tophat_fusion_post.xml @ 4:51ede4e7d4f0

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Add Tophat2 requirement.
author devteam@galaxyproject.org
date Mon, 10 Feb 2014 12:42:02 -0500
parents 2f75d0317ee5
children 052b357bb2b8
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3:2f75d0317ee5 4:51ede4e7d4f0
1 <tool id="tophat_fusion_post" name="Tophat Fusion Post" version="0.1"> 1 <tool id="tophat_fusion_post" name="Tophat Fusion Post" version="0.1">
2 <description>post-processing to identify fusion genes</description> 2 <description>post-processing to identify fusion genes</description>
3 <version_command>tophat-fusion-post --version</version_command> 3 <version_command>tophat-fusion-post --version</version_command>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.2.28">blast+</requirement> 5 <requirement type="package" version="2.2.28">blast+</requirement>
6 <requirement type='package' version="0.12.7">bowtie</requirement> 6 <requirement type="package" version="0.12.7">bowtie</requirement>
7 <requirement type="package" version="2.0.9">tophat2</requirement>
7 </requirements> 8 </requirements>
8 <command> 9 <command>
9 ## Set up tophat_out structure. 10 ## Set up tophat_out structure.
10 mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out; 11 mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out;
11 12